--- a/Gff3.py	Wed Jul 20 12:29:08 2016 -0400
+++ b/Gff3.py	Thu Jul 21 05:58:51 2016 -0400
@@ -11,11 +11,8 @@
 
 
 class Gff3( Datatype ):
-    def __init__( self, input_Gff3_false_path, data_gff3,
-                  input_fasta_false_path, extra_files_path, tool_directory ):
-        super( Gff3, self ).__init__(
-                input_fasta_false_path, extra_files_path, tool_directory
-        )
+    def __init__(self, input_Gff3_false_path, data_gff3):
+        super( Gff3, self ).__init__()
 
         self.track = None
 
@@ -29,8 +26,6 @@
         sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
 
         # TODO: Refactor into another Class to manage the twoBitInfo and ChromSizes (same process as in Gtf.py)
-        twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0)
-        chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes")
 
         # gff3ToGenePred processing
         subtools.gff3ToGenePred(self.input_Gff3_false_path, genePredFile.name)
@@ -42,19 +37,14 @@
         # Sort processing
         subtools.sort(unsortedBedFile.name, sortedBedFile.name)
 
-        # Generate the twoBitInfo
-        subtools.twoBitInfo(self.twoBitFile.name, twoBitInfoFile.name)
-
-        # Then we get the output to generate the chromSizes
         # TODO: Check if no errors
-        subtools.sortChromSizes(twoBitInfoFile.name, chromSizesFile.name)
 
         # bedToBigBed processing
         # TODO: Change the name of the bb, to tool + genome + possible adding if multiple +  .bb
         trackName = "".join( (self.name_gff3, ".bb" ) )
         myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
         with open(myBigBedFilePath, 'w') as bigBedFile:
-            subtools.bedToBigBed(sortedBedFile.name, chromSizesFile.name, bigBedFile.name)
+            subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name)
 
         # Create the Track Object
         dataURL = "tracks/%s" % trackName